Most future projections forecast significant and ongoing climate change during the 21st century, but with the severity of impacts dependent on efforts to restrain or reorganise human activity to limit carbon dioxide (CO2) emissions. A major sink for atmospheric CO2, and a key source of biological resources, the World Ocean is widely anticipated to undergo profound physical and – via ocean acidification – chemical changes as direct and indirect results of these emissions. Given strong biophysical coupling, the marine biota is also expected to experience strong changes in response to this anthropogenic forcing. Here we examine the large-scale response of ocean biogeochemistry to climate and acidification impacts during the 21st century for Representative Concentration Pathways (RCPs) 2.6 and 8.5 using an intermediate complexity global ecosystem model, MEDUSA-2.0. The primary impact of future change lies in stratification-led declines in the availability of key nutrients in surface waters, which in turn leads to a global decrease (1990s vs. 2090s) in ocean productivity (−6.3%). This impact has knock-on consequences for the abundance of the low trophic level biogeochemical actors modelled by MEDUSA-2.0 (−5.8%), and these would be expected to similarly impact higher trophic level elements such as fisheries. Related impacts are found in the flux of organic material to seafloor communities (−40.7% at 1000 m), and in the volume of ocean suboxic zones (+12.5%). A sensitivity analysis removing an acidification feedback on calcification finds that change in this process significantly impacts benthic communities, suggesting that a~better understanding of the OA-sensitivity of calcifying organisms, and their role in ballasting sinking organic carbon, may significantly improve forecasting of these ecosystems. For all processes, there is geographical variability in change – for instance, productivity declines −21% in the Atlantic and increases +59% in the Arctic – and changes are much more pronounced under RCP 8.5 than the RCP 2.6 scenario.